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The structure determination of surface species has long been a challenge because of their rich chemical heterogeneities. Modern tip-based microscopic techniques can resolve heterogeneities from their distinct electronic, geometric, and vibrational properties at the single-molecule level but with limited interpretation from each. Here, we combined scanning tunneling microscopy (STM), noncontact atomic force microscopy (AFM), and tip-enhanced Raman scattering (TERS) to characterize an assumed inactive system, pentacene on the Ag(110) surface. This enabled us to unambiguously correlate the structural and chemical heterogeneities of three pentacene-derivative species through specific carbon-hydrogen bond breaking. The joint STM-AFM-TERS strategy provides a comprehensive solution for determining chemical structures that are widely present in surface catalysis, on-surface synthesis, and two-dimensional materials.